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2VJX
Biol. Unit 2
Info
Asym.Unit (314 KB)
Biol.Unit 1 (158 KB)
Biol.Unit 2 (156 KB)
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(1)
Title
:
STRUCTURAL AND BIOCHEMICAL EVIDENCE FOR A BOAT-LIKE TRANSITION STATE IN BETA-MANNOSIDASES
Authors
:
L. E. Tailford, W. A. Offen, N. L. Smith, C. Dumon, C. Moreland, J. Gratien, M. P. Heck, R. V. Stick, Y. Bleriot, A. Vasella, H. J. Gilbert, G. J. Davies
Date
:
14 Dec 07 (Deposition) - 01 Apr 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Linear Free Energy Relationship, Hydrolase, Transition State Mimic, Mannosidase, Glycoside Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. E. Tailford, W. A. Offen, N. L. Smith, C. Dumon, C. Moreland, J. Gratien, M. P. Heck, R. V. Stick, Y. Bleriot, A. Vasella, H. J. Gilbert, G. J. Davies
Structural And Biochemical Evidence For A Boat-Like Transition State In Beta-Mannosidases.
Nat. Chem. Biol. V. 4 306 2008
[
close entry info
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Hetero Components
(2, 22)
Info
All Hetero Components
1a: BROMIDE ION (BRa)
1b: BROMIDE ION (BRb)
1c: BROMIDE ION (BRc)
1d: BROMIDE ION (BRd)
1e: BROMIDE ION (BRe)
1f: BROMIDE ION (BRf)
1g: BROMIDE ION (BRg)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
2g: CHLORIDE ION (CLg)
2h: CHLORIDE ION (CLh)
2i: CHLORIDE ION (CLi)
2j: CHLORIDE ION (CLj)
2k: CHLORIDE ION (CLk)
2l: CHLORIDE ION (CLl)
3a: 1,2-ETHANEDIOL (EDOa)
3aa: 1,2-ETHANEDIOL (EDOaa)
3ab: 1,2-ETHANEDIOL (EDOab)
3ac: 1,2-ETHANEDIOL (EDOac)
3ad: 1,2-ETHANEDIOL (EDOad)
3ae: 1,2-ETHANEDIOL (EDOae)
3af: 1,2-ETHANEDIOL (EDOaf)
3ag: 1,2-ETHANEDIOL (EDOag)
3ah: 1,2-ETHANEDIOL (EDOah)
3ai: 1,2-ETHANEDIOL (EDOai)
3aj: 1,2-ETHANEDIOL (EDOaj)
3ak: 1,2-ETHANEDIOL (EDOak)
3al: 1,2-ETHANEDIOL (EDOal)
3am: 1,2-ETHANEDIOL (EDOam)
3an: 1,2-ETHANEDIOL (EDOan)
3ao: 1,2-ETHANEDIOL (EDOao)
3ap: 1,2-ETHANEDIOL (EDOap)
3aq: 1,2-ETHANEDIOL (EDOaq)
3ar: 1,2-ETHANEDIOL (EDOar)
3as: 1,2-ETHANEDIOL (EDOas)
3at: 1,2-ETHANEDIOL (EDOat)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
3h: 1,2-ETHANEDIOL (EDOh)
3i: 1,2-ETHANEDIOL (EDOi)
3j: 1,2-ETHANEDIOL (EDOj)
3k: 1,2-ETHANEDIOL (EDOk)
3l: 1,2-ETHANEDIOL (EDOl)
3m: 1,2-ETHANEDIOL (EDOm)
3n: 1,2-ETHANEDIOL (EDOn)
3o: 1,2-ETHANEDIOL (EDOo)
3p: 1,2-ETHANEDIOL (EDOp)
3q: 1,2-ETHANEDIOL (EDOq)
3r: 1,2-ETHANEDIOL (EDOr)
3s: 1,2-ETHANEDIOL (EDOs)
3t: 1,2-ETHANEDIOL (EDOt)
3u: 1,2-ETHANEDIOL (EDOu)
3v: 1,2-ETHANEDIOL (EDOv)
3w: 1,2-ETHANEDIOL (EDOw)
3x: 1,2-ETHANEDIOL (EDOx)
3y: 1,2-ETHANEDIOL (EDOy)
3z: 1,2-ETHANEDIOL (EDOz)
4a: (3S,4R,5R)-3,4-DIHYDROXY-5-(HYDROX... (IFLa)
4b: (3S,4R,5R)-3,4-DIHYDROXY-5-(HYDROX... (IFLb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BR
-1
Ligand/Ion
BROMIDE ION
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
EDO
21
Ligand/Ion
1,2-ETHANEDIOL
4
IFL
1
Ligand/Ion
(3S,4R,5R)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)PIPERIDIN-2-ONE
[
close Hetero Component info
]
Sites
(33, 33)
Info
All Sites
01: AC2 (SOFTWARE)
02: AC4 (SOFTWARE)
03: BC2 (SOFTWARE)
04: BC3 (SOFTWARE)
05: BC5 (SOFTWARE)
06: BC8 (SOFTWARE)
07: BC9 (SOFTWARE)
08: CC1 (SOFTWARE)
09: CC3 (SOFTWARE)
10: CC6 (SOFTWARE)
11: CC7 (SOFTWARE)
12: CC8 (SOFTWARE)
13: CC9 (SOFTWARE)
14: DC4 (SOFTWARE)
15: DC8 (SOFTWARE)
16: EC1 (SOFTWARE)
17: EC2 (SOFTWARE)
18: EC3 (SOFTWARE)
19: EC4 (SOFTWARE)
20: EC5 (SOFTWARE)
21: EC7 (SOFTWARE)
22: EC9 (SOFTWARE)
23: FC2 (SOFTWARE)
24: FC4 (SOFTWARE)
25: FC6 (SOFTWARE)
26: FC7 (SOFTWARE)
27: FC8 (SOFTWARE)
28: GC3 (SOFTWARE)
29: GC4 (SOFTWARE)
30: GC5 (SOFTWARE)
31: GC9 (SOFTWARE)
32: HC1 (SOFTWARE)
33: HC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC2
SOFTWARE
TRP B:198 , ASP B:199 , TRP B:200 , TRP B:395 , CYS B:424 , ASN B:461 , GLU B:462 , TRP B:533 , TYR B:537 , GLU B:555 , TRP B:645 , EDO B:1877
BINDING SITE FOR RESIDUE IFL B1867
02
AC4
SOFTWARE
TRP B:525 , SER B:530 , ASN B:532 , ASP B:548 , LEU B:549 , PRO B:550 , MET B:553 , HOH B:2621
BINDING SITE FOR RESIDUE EDO B1868
03
BC2
SOFTWARE
ASN B:337 , VAL B:510 , HIS B:511 , TYR B:515 , HOH B:2622 , HOH B:2623 , HOH B:2624
BINDING SITE FOR RESIDUE EDO B1869
04
BC3
SOFTWARE
TYR A:155 , HIS A:157 , ASP B:88 , HIS B:157 , GLN B:162 , EDO B:1885
BINDING SITE FOR RESIDUE EDO B1870
05
BC5
SOFTWARE
THR A:432 , HOH A:2093 , LEU B:126 , LEU B:127 , LYS B:129
BINDING SITE FOR RESIDUE EDO B1871
06
BC8
SOFTWARE
SER B:43 , GLN B:44 , SER B:45 , GLY B:46 , THR B:47 , GLU B:48 , GLU B:90 , HOH B:2625
BINDING SITE FOR RESIDUE EDO B1872
07
BC9
SOFTWARE
TYR A:117 , ALA A:118 , ASP A:119 , LYS A:129 , ALA A:130 , HIS A:157 , BR A:1893 , HOH A:2628 , HOH A:2629 , LYS B:129
BINDING SITE FOR RESIDUE EDO A1876
08
CC1
SOFTWARE
PHE B:542 , GLU B:543 , ASP B:603 , GLY B:624 , HOH B:2499
BINDING SITE FOR RESIDUE EDO B1873
09
CC3
SOFTWARE
ARG B:331 , ASP B:506 , ARG B:507 , HOH B:2287 , HOH B:2626
BINDING SITE FOR RESIDUE EDO B1874
10
CC6
SOFTWARE
GLN B:365 , ASN B:648 , ASP B:649 , ILE B:659 , ASP B:660
BINDING SITE FOR RESIDUE EDO B1875
11
CC7
SOFTWARE
GLU B:465 , LYS B:468 , TYR B:469 , PRO B:514 , LEU B:516 , ALA B:517
BINDING SITE FOR RESIDUE EDO B1876
12
CC8
SOFTWARE
ASN B:178 , ASP B:199 , CYS B:424 , GLU B:462 , TRP B:470 , IFL B:1867
BINDING SITE FOR RESIDUE EDO B1877
13
CC9
SOFTWARE
ASP A:88 , HIS A:157 , GLN A:162 , EDO A:1888 , TYR B:155 , HIS B:157
BINDING SITE FOR RESIDUE EDO A1880
14
DC4
SOFTWARE
PHE B:356 , ARG B:633 , ARG B:636 , ILE B:695 , SER B:696 , ASP B:697 , ASN B:733 , THR B:734
BINDING SITE FOR RESIDUE EDO B1878
15
DC8
SOFTWARE
ILE B:328 , GLY B:329 , ARG B:449 , ASN B:450 , HIS B:451 , ALA B:452 , ARG B:507
BINDING SITE FOR RESIDUE EDO B1879
16
EC1
SOFTWARE
LEU B:819 , GLN B:820 , ARG B:845
BINDING SITE FOR RESIDUE EDO B1880
17
EC2
SOFTWARE
PHE B:775 , ARG B:777 , CL B:1889 , HOH B:2627
BINDING SITE FOR RESIDUE EDO B1881
18
EC3
SOFTWARE
ARG A:161 , GLN A:162 , PRO A:165 , EDO A:1880 , ASP B:119 , TYR B:121 , TYR B:155
BINDING SITE FOR RESIDUE EDO A1888
19
EC4
SOFTWARE
PHE B:42 , SER B:43 , GLN B:44 , THR B:47 , LYS B:49 , MET B:51 , LEU B:68
BINDING SITE FOR RESIDUE EDO B1882
20
EC5
SOFTWARE
PRO B:212 , HOH B:2074 , HOH B:2344 , HOH B:2628
BINDING SITE FOR RESIDUE EDO B1883
21
EC7
SOFTWARE
ARG B:382 , ARG B:823 , SER B:825 , ILE B:840 , THR B:842 , HOH B:2629 , HOH B:2630
BINDING SITE FOR RESIDUE EDO B1884
22
EC9
SOFTWARE
ASP A:119 , TYR A:121 , TYR A:155 , ARG B:161 , GLN B:162 , PRO B:165 , EDO B:1870
BINDING SITE FOR RESIDUE EDO B1885
23
FC2
SOFTWARE
ILE B:107 , LYS B:142
BINDING SITE FOR RESIDUE BR B1886
24
FC4
SOFTWARE
LYS A:129 , HIS A:157 , EDO A:1876 , LYS B:129 , HIS B:157 , GLN B:162
BINDING SITE FOR RESIDUE BR A1893
25
FC6
SOFTWARE
GLN B:685 , ASP B:688
BINDING SITE FOR RESIDUE BR B1887
26
FC7
SOFTWARE
GLN B:108
BINDING SITE FOR RESIDUE CL B1888
27
FC8
SOFTWARE
GLN B:685 , HIS B:774 , EDO B:1881 , HOH B:2531
BINDING SITE FOR RESIDUE CL B1889
28
GC3
SOFTWARE
HOH B:2624
BINDING SITE FOR RESIDUE CL B1895
29
GC4
SOFTWARE
ASN B:300 , ASN B:390 , HOH B:2308
BINDING SITE FOR RESIDUE CL B1890
30
GC5
SOFTWARE
ASP B:131 , ASN B:132 , ARG B:436 , HOH B:2109
BINDING SITE FOR RESIDUE CL B1891
31
GC9
SOFTWARE
ARG B:376 , TYR B:661
BINDING SITE FOR RESIDUE EDO B1892
32
HC1
SOFTWARE
ARG B:597 , PRO B:607 , GLU B:608 , SER B:609 , PHE B:613 , HOH B:2631
BINDING SITE FOR RESIDUE EDO B1893
33
HC2
SOFTWARE
GLN B:623 , ARG B:626 , HIS B:774 , PHE B:775 , HOH B:2569 , HOH B:2627 , HOH B:2632 , HOH B:2633
BINDING SITE FOR RESIDUE EDO B1894
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 10)
Info
All SCOP Domains
1a: SCOP_d2vjxa4 (A:28-219)
1b: SCOP_d2vjxb4 (B:28-219)
2a: SCOP_d2vjxa1 (A:220-330)
2b: SCOP_d2vjxa2 (A:784-864)
2c: SCOP_d2vjxa3 (A:679-783)
2d: SCOP_d2vjxb1 (B:220-330)
2e: SCOP_d2vjxb2 (B:784-866)
2f: SCOP_d2vjxb3 (B:679-783)
3a: SCOP_d2vjxa5 (A:331-678)
3b: SCOP_d2vjxb5 (B:331-678)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Galactose-binding domain-like
(314)
Superfamily
:
Galactose-binding domain-like
(314)
Family
:
automated matches
(85)
Protein domain
:
automated matches
(85)
Bacteroides thetaiotaomicron [TaxId: 226186]
(7)
1a
d2vjxa4
A:28-219
1b
d2vjxb4
B:28-219
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
beta-Galactosidase/glucuronidase domain
(79)
Family
:
automated matches
(30)
Protein domain
:
automated matches
(30)
Bacteroides thetaiotaomicron [TaxId: 226186]
(7)
2a
d2vjxa1
A:220-330
2b
d2vjxa2
A:784-864
2c
d2vjxa3
A:679-783
2d
d2vjxb1
B:220-330
2e
d2vjxb2
B:784-866
2f
d2vjxb3
B:679-783
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
(Trans)glycosidases
(1191)
Family
:
beta-glycanases
(284)
Protein domain
:
automated matches
(49)
Bacteroides thetaiotaomicron [TaxId: 226186]
(7)
3a
d2vjxa5
A:331-678
3b
d2vjxb5
B:331-678
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
[
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Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_2_N_2vjxB01 (B:28-219)
1b: PFAM_Glyco_hydro_2_N_2vjxB02 (B:28-219)
2a: PFAM_Glyco_hydro_2_C_2vjxB03 (B:345-478)
2b: PFAM_Glyco_hydro_2_C_2vjxB04 (B:345-478)
3a: PFAM_Glyco_hydro_2_2vjxB05 (B:221-331)
3b: PFAM_Glyco_hydro_2_2vjxB06 (B:221-331)
View:
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Clans
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Families
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Organisms
(
)
(
)
Clan
:
GBD
(153)
Family
:
Glyco_hydro_2_N
(32)
Bacteroides thetaiotaomicron
(9)
1a
Glyco_hydro_2_N-2vjxB01
B:28-219
1b
Glyco_hydro_2_N-2vjxB02
B:28-219
Clan
:
Glyco_hydro_tim
(488)
Family
:
Glyco_hydro_2_C
(27)
Bacteroides thetaiotaomicron
(9)
2a
Glyco_hydro_2_C-2vjxB03
B:345-478
2b
Glyco_hydro_2_C-2vjxB04
B:345-478
Clan
:
no clan defined [family: Glyco_hydro_2]
(31)
Family
:
Glyco_hydro_2
(31)
Bacteroides thetaiotaomicron
(9)
3a
Glyco_hydro_2-2vjxB05
B:221-331
3b
Glyco_hydro_2-2vjxB06
B:221-331
[
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